Wow, I will have to digest this a bit.
1) In Live, are you using MIDI remote Script (top section of MIDI) for port 1, user port or both?
2) Does Squarp send to Ableton as just an instrument (track) or also as a control surface?
3) How is your BomeBox going to play into this? What devices will be connected. Is BomeBox replacing MOTU?
4) Is your USB hub powered? (it should be since you have 4 devices connected)
1) Define only one alias per device. Creating multiple aliases for the same device will bite you sooner or later.
2) MT Pro opens and closes ports automatically as they are needed. If you want to hold a port open all of the time, you should put a check mark by that port's alias at the project level to ensure the port is always held open. Do not also put a check mark by the physical port. The alias will handling the control of the physical port.
3) Only use thru paths in the static router if:
Most everything needs to go through that path untouched
You have variable length Sysex that you cannot manage with translators
Note that if you have a static path defined EVERYTHING will go through that path unless you have a translator that executes an outgoing action and the option "SWALLOW" is set.
For instance, if the translator has a rule like "if xx==yy then exit rules, skip outgoing action", then swallow will not work. In this case you need to set up another translator with the exact same incoming trigger and an outgoing action of none. Otherwise the message will still go through.
4) Organize your presets by device. Put all translator with the same input and output path under it's parent preset. You can have presets that have multiple output devices. If so, use their aliases, not their physical port. If you have a few exceptions (maybe one or two translators). You can override the preset (and project) paths within a translator, but do so sparingly.
5) Give your aliases meaning full names so you don't trip yourself up. I usually name my aliases "From xxx" or "To xx" to make it clear whether it is an input or output alias. Using a term like "MIDI DIN", may end up being confusing even if the device is currently on a MIDI DIN port. Maybe in the future it will be on a network or USB port and so naming it MIDI DIN would be confusing if you change to a configuration like that.
For your aliases based on the diagram I will use something like:
From Push Port 1
To Push Port 1
From Push User Port
To Push User Port
From Pyramid Squarp
To Pyramid Squarm
From Live Control
To Live Control
From Live Instrument
To Live Instrument
From Juno 106
To Juno 106
For Clock I would just set up a preset (or maybe just a single translator) with defined inputs and outputs
Input: From Pyramid Squarp
To Live Control
To Juno 106
Notice I picked the Aliases from existing ones above.
For me, I alway prefer to use translators and seldom every use static thru paths. I've been bitten too many times in the past with the Swallow rule I mentioned earlier and prefer to have absolute control.
Bome Q and A Moderator and
Independent Bome Consultant/Specialist